Structure

Physi-Chem Properties

Molecular Weight:  213.1
Volume:  211.208
LogP:  0.698
LogD:  1.079
LogS:  -1.289
# Rotatable Bonds:  6
TPSA:  82.7
# H-Bond Aceptor:  5
# H-Bond Donor:  3
# Rings:  1
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.691
Synthetic Accessibility Score:  3.191
Fsp3:  0.5
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.715
MDCK Permeability:  1.4176993317960296e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.147
Human Intestinal Absorption (HIA):  0.022
20% Bioavailability (F20%):  0.015
30% Bioavailability (F30%):  0.196

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.989
Plasma Protein Binding (PPB):  71.32625579833984%
Volume Distribution (VD):  0.682
Pgp-substrate:  47.027000427246094%

ADMET: Metabolism

CYP1A2-inhibitor:  0.043
CYP1A2-substrate:  0.218
CYP2C19-inhibitor:  0.039
CYP2C19-substrate:  0.281
CYP2C9-inhibitor:  0.148
CYP2C9-substrate:  0.857
CYP2D6-inhibitor:  0.007
CYP2D6-substrate:  0.256
CYP3A4-inhibitor:  0.01
CYP3A4-substrate:  0.193

ADMET: Excretion

Clearance (CL):  15.144
Half-life (T1/2):  0.89

ADMET: Toxicity

hERG Blockers:  0.009
Human Hepatotoxicity (H-HT):  0.152
Drug-inuced Liver Injury (DILI):  0.155
AMES Toxicity:  0.024
Rat Oral Acute Toxicity:  0.538
Maximum Recommended Daily Dose:  0.047
Skin Sensitization:  0.482
Carcinogencity:  0.855
Eye Corrosion:  0.005
Eye Irritation:  0.067
Respiratory Toxicity:  0.293

Download Data

Data Type Select
General Info & Identifiers & Properties  
Structure MOL file  
Source Organisms  
Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC145658

Natural Product ID:  NPC145658
Common Name*:   N-(3-Oxohexanoyl)-L-Homoserine Lactone
IUPAC Name:   3-oxo-N-[(3S)-2-oxooxolan-3-yl]hexanamide
Synonyms:  
Standard InCHIKey:  YRYOXRMDHALAFL-QMMMGPOBSA-N
Standard InCHI:  InChI=1S/C10H15NO4/c1-2-3-7(12)6-9(13)11-8-4-5-15-10(8)14/h8H,2-6H2,1H3,(H,11,13)/t8-/m0/s1
SMILES:  CCCC(=O)CC(=N[C@H]1CCOC1=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL458201
PubChem CID:   688505
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0000013] Amino acids, peptides, and analogues
          • [CHEMONTID:0000347] Amino acids and derivatives
            • [CHEMONTID:0000060] Alpha amino acids and derivatives
              • [CHEMONTID:0001189] N-acyl-alpha amino acids and derivatives

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO32854 vibrio angustum s14 Species Vibrionaceae Bacteria n.a. n.a. n.a. PMID[11325243]

☑ Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

  NP Quantity Composition/Concentration

Organism ID NP ID Organism Material Preparation Organism Part NP Quantity (Standard) NP Quantity (Minimum) NP Quantity (Maximum) Quantity Unit Reference

☑ Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

  Biological Activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT4195 Individual Protein Transcriptional activator protein lasR Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG12228) IC50 = 40000.0 nM PMID[567231]
NPT2 Others Unspecified EC50 > 10000.0 nM PMID[567230]
NPT2 Others Unspecified IC50 = 10400.0 nM PMID[567231]
NPT2 Others Unspecified EC50 > 100000.0 nM PMID[567231]

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

  Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

●  The left chart: Distribution of similarity level between NPC145658 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID
0.9062 High Similarity NPC477642
0.8788 High Similarity NPC477641
0.8788 High Similarity NPC477643
0.8788 High Similarity NPC320865
0.8689 High Similarity NPC477644
0.8361 Intermediate Similarity NPC473599
0.7536 Intermediate Similarity NPC473985
0.7536 Intermediate Similarity NPC475808
0.7536 Intermediate Similarity NPC474299
0.7536 Intermediate Similarity NPC28348
0.7536 Intermediate Similarity NPC474298
0.7183 Intermediate Similarity NPC478256
0.68 Remote Similarity NPC472595
0.6721 Remote Similarity NPC227850
0.6712 Remote Similarity NPC476291
0.6712 Remote Similarity NPC476285
0.6667 Remote Similarity NPC43219
0.6627 Remote Similarity NPC477728
0.6623 Remote Similarity NPC472594
0.662 Remote Similarity NPC470108
0.6579 Remote Similarity NPC86064
0.6533 Remote Similarity NPC141325
0.6528 Remote Similarity NPC470109
0.6471 Remote Similarity NPC254541
0.6463 Remote Similarity NPC95478
0.6463 Remote Similarity NPC155670
0.6463 Remote Similarity NPC145748
0.6447 Remote Similarity NPC476248
0.6447 Remote Similarity NPC138435
0.6438 Remote Similarity NPC470110
0.6429 Remote Similarity NPC327252
0.6406 Remote Similarity NPC322946
0.6386 Remote Similarity NPC227051
0.6364 Remote Similarity NPC322573
0.6364 Remote Similarity NPC327831
0.6351 Remote Similarity NPC314273
0.6351 Remote Similarity NPC193280
0.6341 Remote Similarity NPC474312
0.6341 Remote Similarity NPC477730
0.6338 Remote Similarity NPC57420
0.6324 Remote Similarity NPC176164
0.6324 Remote Similarity NPC189301
0.6308 Remote Similarity NPC329495
0.6308 Remote Similarity NPC263065
0.6308 Remote Similarity NPC189178
0.6282 Remote Similarity NPC476130
0.6282 Remote Similarity NPC476324
0.625 Remote Similarity NPC329181
0.625 Remote Similarity NPC327239
0.625 Remote Similarity NPC319110
0.6232 Remote Similarity NPC320598
0.6154 Remote Similarity NPC29950
0.6154 Remote Similarity NPC19576
0.6125 Remote Similarity NPC316242
0.6104 Remote Similarity NPC474403
0.6098 Remote Similarity NPC314466
0.6081 Remote Similarity NPC118524
0.6049 Remote Similarity NPC473984
0.6049 Remote Similarity NPC315131
0.6049 Remote Similarity NPC315535
0.6049 Remote Similarity NPC478017
0.6029 Remote Similarity NPC325985
0.6029 Remote Similarity NPC38463
0.6023 Remote Similarity NPC477729
0.6 Remote Similarity NPC321468
0.6 Remote Similarity NPC316826
0.6 Remote Similarity NPC321536
0.6 Remote Similarity NPC317143
0.6 Remote Similarity NPC327748
0.597 Remote Similarity NPC321118
0.597 Remote Similarity NPC316889
0.5942 Remote Similarity NPC318260
0.5942 Remote Similarity NPC317147
0.5938 Remote Similarity NPC153370
0.5921 Remote Similarity NPC474812
0.5915 Remote Similarity NPC329564
0.5915 Remote Similarity NPC327170
0.5915 Remote Similarity NPC143722
0.5904 Remote Similarity NPC475542
0.5897 Remote Similarity NPC55274
0.5873 Remote Similarity NPC297220
0.5846 Remote Similarity NPC270805
0.5846 Remote Similarity NPC328378
0.5846 Remote Similarity NPC93888
0.5843 Remote Similarity NPC475801
0.5843 Remote Similarity NPC474593
0.5811 Remote Similarity NPC472609
0.5811 Remote Similarity NPC160661
0.5797 Remote Similarity NPC313263
0.5781 Remote Similarity NPC181588
0.5778 Remote Similarity NPC474576
0.5765 Remote Similarity NPC47135
0.5765 Remote Similarity NPC469833
0.5765 Remote Similarity NPC469838
0.5732 Remote Similarity NPC37681
0.573 Remote Similarity NPC193386
0.573 Remote Similarity NPC292345
0.5714 Remote Similarity NPC62263
0.5714 Remote Similarity NPC208537
0.5714 Remote Similarity NPC270005
0.5714 Remote Similarity NPC471098
0.5714 Remote Similarity NPC173763
0.5696 Remote Similarity NPC315897
0.5694 Remote Similarity NPC471129
0.5679 Remote Similarity NPC470782
0.5676 Remote Similarity NPC289691
0.5676 Remote Similarity NPC315744
0.5667 Remote Similarity NPC327250
0.5663 Remote Similarity NPC474833
0.5652 Remote Similarity NPC471917
0.5641 Remote Similarity NPC327753
0.5641 Remote Similarity NPC327486
0.5641 Remote Similarity NPC223174
0.5634 Remote Similarity NPC190385
0.5634 Remote Similarity NPC328447
0.5625 Remote Similarity NPC306238
0.5625 Remote Similarity NPC248970
0.56 Remote Similarity NPC174304
0.56 Remote Similarity NPC325597

  Chemically structural similarity: II. Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

●  The left chart: Distribution of similarity level between NPC145658 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
0.8788 High Similarity NPD2256 Clinical (unspecified phase)
0.8448 Intermediate Similarity NPD9419 Clinical (unspecified phase)
0.6806 Remote Similarity NPD3724 Clinical (unspecified phase)
0.6711 Remote Similarity NPD1453 Phase 1
0.6538 Remote Similarity NPD3160 Suspended
0.6528 Remote Similarity NPD2263 Discontinued
0.6522 Remote Similarity NPD574 Approved
0.6429 Remote Similarity NPD575 Clinical (unspecified phase)
0.641 Remote Similarity NPD2689 Clinical (unspecified phase)
0.6406 Remote Similarity NPD9441 Phase 2
0.64 Remote Similarity NPD9446 Approved
0.6324 Remote Similarity NPD9433 Approved
0.6308 Remote Similarity NPD9204 Approved
0.6308 Remote Similarity NPD9205 Approved
0.622 Remote Similarity NPD1448 Clinical (unspecified phase)
0.6154 Remote Similarity NPD8846 Approved
0.6154 Remote Similarity NPD61 Approved
0.6154 Remote Similarity NPD8847 Approved
0.6111 Remote Similarity NPD8394 Approved
0.6081 Remote Similarity NPD1429 Clinical (unspecified phase)
0.6049 Remote Similarity NPD7917 Clinical (unspecified phase)
0.6049 Remote Similarity NPD7918 Clinical (unspecified phase)
0.6029 Remote Similarity NPD9659 Approved
0.5938 Remote Similarity NPD8614 Approved
0.593 Remote Similarity NPD619 Phase 3
0.589 Remote Similarity NPD364 Discontinued
0.5875 Remote Similarity NPD376 Approved
0.5875 Remote Similarity NPD11 Approved
0.5846 Remote Similarity NPD8624 Approved
0.5824 Remote Similarity NPD1446 Phase 3
0.5824 Remote Similarity NPD1447 Phase 3
0.5781 Remote Similarity NPD8810 Clinical (unspecified phase)
0.5765 Remote Similarity NPD7345 Approved
0.5758 Remote Similarity NPD329 Discontinued
0.5735 Remote Similarity NPD630 Approved
0.5735 Remote Similarity NPD631 Approved
0.573 Remote Similarity NPD618 Clinical (unspecified phase)
0.5714 Remote Similarity NPD1815 Discontinued
0.5696 Remote Similarity NPD1825 Clinical (unspecified phase)
0.5696 Remote Similarity NPD6944 Clinical (unspecified phase)
0.5676 Remote Similarity NPD1151 Approved
0.5667 Remote Similarity NPD3716 Discontinued
0.5658 Remote Similarity NPD8842 Clinical (unspecified phase)
0.5658 Remote Similarity NPD886 Clinical (unspecified phase)
0.5641 Remote Similarity NPD9445 Approved
0.5634 Remote Similarity NPD9661 Approved
0.5634 Remote Similarity NPD9023 Clinical (unspecified phase)
0.5625 Remote Similarity NPD1152 Phase 2
0.5625 Remote Similarity NPD8870 Approved
0.5606 Remote Similarity NPD9016 Clinical (unspecified phase)
0.5604 Remote Similarity NPD4780 Clinical (unspecified phase)
0.56 Remote Similarity NPD348 Approved

  Bioactivity similarity: Similar Natural Products in NPASS

Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.

Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity
B: biological targets similarity
C: networks similarity
D: cell-based bioactivity similarity
E: similarity based on clinical data